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"Application/website recommendations are off-topic and out of scope. It is better instead to use a particular web app or website and ask for help in any issues you have with it specifically." – Al E., Alex, Eight Days of Malaise, jonsca

2 Answers
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The best hotel deals so far I've found on hotwire.com. They have an API as well. We did use them to plan a road trip while on the road :). I don't believe they offer vacancy data though (of course, this being hotwire, you won't know what hotel you're booking until you've booked it - but no disappointments yet).